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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ), 'gf_id' => 'HOM05D001269', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001269' ), 'data_identifier' => 'HOM05D001269', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001269', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '493', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p02150' => 'bna', 'A03p06160' => 'bna', 'A08p13110' => 'bna', 'A10p24580' => 'bna', 'Aa31sc362G10' => 'aar', 'Aa31sc90G20' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.393' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5798' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.5802' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.162' => 'aag', 'Actinidia12706' => 'ach', 'Actinidia32067' => 'ach', 'Actinidia32802' => 'ach', 'Ah.04g149560' => 'amhyb', 'Ah.04g150000' => 'amhyb', 'AL5G21760' => 'aly', 'AL6G24350' => 'aly', 'AL6G24370' => 'aly', 'AL6G24600' => 'aly', 'Aqoxy2G00179_Aqoxy2G00180_Aqoxy2G00182' => 'aox', 'Aqoxy2G00185' => 'aox', 'Aqoxy2G00186' => 'aox', 'arahy.Tifrunner.gnm1.ann1.C5IAZ7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GT3YU4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IC07XZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JH2NJV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U7JD1F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.U8R2BF' => 'arhy', 'AT3G43790' => 'ath', 'AT5G13740' => 'ath', 'AT5G13750' => 'ath', 'ATR1096G021' => 'atr', 'ATR1096G076' => 'atr', 'ATR1096G114' => 'atr', 'ATR1096G144' => 'atr', 'Atru.chr10.801' => 'acertr', 'Atru.chr12.1097' => 'acertr', 'Atru.chr12.1100' => 'acertr', 'Atru.chr12.1105' => 'acertr', 'Atru.chr8.923' => 'acertr', 'AUR62018452' => 'cqu', 'AUR62020967' => 'cqu', 'AUR62032823' => 'cqu', 'AUR62034113' => 'cqu', 'AUR62041280' => 'cqu', 'BcaB01g05338' => 'bca', 'BcaB01g05339' => 'bca', 'BcaB06g27007' => 'bca', 'BcaC04g19020' => 'bca', 'BcaC04g19025' => 'bca', 'BcaC04g19083' => 'bca', 'BcaC04g19088' => 'bca', 'BcaC04g24257' => 'bca', 'BcaC04g24258' => 'bca', 'BcaC07g38058' => 'bca', 'BcaC07g38059' => 'bca', 'BcaC07g38063' => 'bca', 'BcaNung04188' => 'bca', 'BolC2t06584H' => 'bol', 'BolC2t06585H' => 'bol', 'BolC3t13217H' => 'bol', 'BolC3t13218H' => 'bol', 'BolC8t48456H' => 'bol', 'BolC8t48457H' => 'bol', 'BolC8t48464H' => 'bol', 'BolC9t59094H' => 'bol', 'BolC9t59101H' => 'bol', 'BolC9t59172H' => 'bol', 'BolC9t59173H' => 'bol', 'BolC9t59180H' => 'bol', 'BolC9t59181H' => 'bol', 'BolC9t59187H' => 'bol', 'BraA02t05186Z' => 'bra', 'BraA02t05187Z' => 'bra', 'BraA02t05188Z' => 'bra', 'BraA02t05189Z' => 'bra', 'BraA03t09949Z' => 'bra', 'BraA03t09950Z' => 'bra', 'BraA08t33290Z' => 'bra', 'BraA10t44521Z' => 'bra', 'C02p06410' => 'bna', 'C03p07170' => 'bna', 'C09p62560' => 'bna', 'C09p62640' => 'bna', 'C09p63330' => 'bna', 'C09p63340' => 'bna', 'C09p63350' => 'bna', 'C09p63410' => 'bna', 'CAN.G128.118' => 'can', 'CAN.G128.120' => 'can', 'CAN.G128.122' => 'can', 'CAN.G134.34' => 'can', 'CAN.G134.35' => 'can', 'CAN.G134.36' => 'can', 'CAN.G134.38' => 'can', 'CAN.G959.44' => 'can', 'CANSAT11G1391' => 'cansat', 'CANSAT54G2837' => 'cansat', 'CANSAT56G3387' => 'cansat', 'CANSAT78G0242' => 'cansat', 'CANSAT78G1059' => 'cansat', 'CANSAT78G1329' => 'cansat', 'CARHR199480' => 'chi', 'CARHR199690' => 'chi', 'CARHR199700' => 'chi', 'Carub.0005s0945' => 'cru', 'Carub.0005s0955' => 'cru', 'Carub.0006s1192' => 'cru', 'Carub.0006s1193' => 'cru', 'Carub.0006s1213' => 'cru', 'Ca_16581_v3' => 'car', 'Ca_18107_v3' => 'car', 'Ca_19745_v3' => 'car', 'Ca_19774_v3' => 'car', 'Ca_25131_v3' => 'car', 'Ca_25853_v3' => 'car', 'Ca_28480_v3' => 'car', 'Cc00_g07000' => 'ccan', 'Cc00_g21290' => 'ccan', 'Cc02_g30820' => 'ccan', 'Cc06_g21170' => 'ccan', 'CDE08G1582' => 'cde', 'Cfa010426' => 'cfa', 'Cfa019901' => 'cfa', 'Cfa024641' => 'cfa', 'Cfa025363' => 'cfa', 'Cfa026512' => 'cfa', 'Cfa027218' => 'cfa', 'Ciclev10001373m.g' => 'ccl', 'Ciclev10003550m.g' => 'ccl', 'CiPaw.09G161400' => 'cil', 'CiPaw.13G048700' => 'cil', 'CiPaw.13G121500' => 'cil', 'ClCG11G013130' => 'cla', 'COL.COLO4_18346' => 'col', 'COL.COLO4_33893' => 'col', 'COL.COLO4_33894' => 'col', 'Cpa.g.sc125.47' => 'cpa', 'Cpa.g.sc1430.1' => 'cpa', 'Cpa.g.sc33.172' => 'cpa', 'Cre12.g512200' => 'cre', 'CsaV3_5G029650' => 'csa', 'CSS0022325' => 'camsi', 'CSS0034806' => 'camsi', 'DCAR_009102' => 'dca', 'DCAR_020620' => 'dca', 'DCAR_024470' => 'dca', 'DCAR_026618' => 'dca', 'DCAR_030801' => 'dca', 'DCAR_030803' => 'dca', 'DCAR_030807' => 'dca', 'DCAR_030808' => 'dca', 'DCAR_030809' => 'dca', 'Dinv04331' => 'din', 'Dinv14540' => 'din', 'Duzib068G0155' => 'dzi', 'Duzib106G0227' => 'dzi', 'Duzib114G0834' => 'dzi', 'Duzib170G1065' => 'dzi', 'ECA232G0464' => 'eca', 'ECA232G3250' => 'eca', 'ECA233G4258' => 'eca', 'ECA238G4012' => 'eca', 'EL10Ac3g07377' => 'bvu', 'EL10Ac4g08813' => 'bvu', 'Eucgr.B03776' => 'egr', 'Eucgr.G02625' => 'egr', 'Eucgr.G02628' => 'egr', 'Eucgr.G02629' => 'egr', 'Eucgr.G02630' => 'egr', 'Eucgr.G02631' => 'egr', 'Eucgr.K01705' => 'egr', 'Eucgr.L01874' => 'egr', 'FAN01G0058' => 'fan', 'FAN03G3130' => 'fan', 'FAN06G3814' => 'fan', 'FAN10G1130' => 'fan', 'FAN14G5003' => 'fan', 'FAN19G1633' => 'fan', 'FAN23G3097' => 'fan', 'FAN28G1051' => 'fan', 'FvH4_1g24560' => 'fve', 'FvH4_7g04820' => 'fve', 'Glyma.04G124800' => 'gma', 'Glyma.06G313500' => 'gma', 'Glyma.06G313600' => 'gma', 'Glyma.06G313700' => 'gma', 'Glyma.13G186400' => 'gma', 'Glyma.13G186500' => 'gma', 'Glyma.13G186600' => 'gma', 'Glyma.13G186700' => 'gma', 'Glyma.15G224200' => 'gma', 'Gohir.A05G102100' => 'ghi', 'Gohir.A05G288100' => 'ghi', 'Gohir.D05G101800' => 'ghi', 'Gohir.D05G289300' => 'ghi', 'Gohir.D09G104700' => 'ghi', 'Gohir.D12G008932' => 'ghi', 'Gorai.005G171100' => 'gra', 'Gorai.006G122900' => 'gra', 'Gorai.008G008900' => 'gra', 'Gorai.008G009000' => 'gra', 'Gorai.009G106000' => 'gra', 'Gorai.009G304400' => 'gra', 'GSVIVG01025827001' => 'vvi', 'GSVIVG01027385001' => 'vvi', 'GSVIVG01027390001' => 'vvi', 'GSVIVG01027391001' => 'vvi', 'GSVIVG01027393001' => 'vvi', 'GSVIVG01027394001' => 'vvi', 'HanXRQChr02g0051191' => 'han', 'HanXRQChr02g0051201' => 'han', 'HanXRQChr04g0115211' => 'han', 'HanXRQChr04g0115231' => 'han', 'HanXRQChr04g0115251' => 'han', 'HanXRQChr04g0115271' => 'han', 'HanXRQChr09g0258181' => 'han', 'HanXRQChr09g0258201' => 'han', 'HanXRQChr09g0258211' => 'han', 'HanXRQChr09g0258221' => 'han', 'HanXRQChr09g0258231' => 'han', 'HanXRQChr13g0406241' => 'han', 'HanXRQChr15g0487261' => 'han', 'Haze_03379' => 'cav', 'Haze_08711' => 'cav', 'Haze_20351' => 'cav', 'Hma1.2p1_1269F.1_g271580' => 'hma', 'Hma1.2p1_1426F.1_g282890' => 'hma', 'HPP92_018384' => 'vpl', 'HPP92_019904' => 'vpl', 'Hund05350' => 'sun', 'Hund05384' => 'sun', 'Hund06833' => 'sun', 'Hund22238' => 'sun', 'Hund24475' => 'sun', 'Hund24479' => 'sun', 'Hund24483' => 'sun', 'Lalb_Chr01g0007561' => 'lal', 'Lalb_Chr03g0032531' => 'lal', 'Lalb_Chr18g0048211' => 'lal', 'Lalb_Chr19g0132701' => 'lal', 'Lalb_Chr19g0132711' => 'lal', 'Lalb_Chr19g0132721' => 'lal', 'Lalb_Chr19g0132731' => 'lal', 'Lalb_Chr19g0132741' => 'lal', 'Lalb_Chr19g0132751' => 'lal', 'Lalb_Chr19g0132761' => 'lal', 'Lalb_Chr19g0132771' => 'lal', 'Lalb_Chr19g0132781' => 'lal', 'Lalb_Chr19g0132801' => 'lal', 'Lalb_Chr19g0132811' => 'lal', 'Lj1g0003730' => 'lja', 'Lj1g0021965' => 'lja', 'Lj2A936T13' => 'lonja', 'Lj2P415T7' => 'lonja', 'Lj3g0001460' => 'lja', 'Lj3g0002808' => 'lja', 'Lj3g0007406' => 'lja', 'Lj3g0012843' => 'lja', 'Lj3g0019011' => 'lja', 'Lj3g0020935' => 'lja', 'Lj3g0028032' => 'lja', 'Lj4g0007930' => 'lja', 'Lj4g0014418' => 'lja', 'Lj9A661T33' => 'lonja', 'Lj9A662T27' => 'lonja', 'Lsat_1_v5_gn_5_65240' => 'lsa', 'Lsat_1_v5_gn_7_94121' => 'lsa', 'Lsat_1_v5_gn_8_117061' => 'lsa', 'Manes.09G001733' => 'mes', 'Manes.10G069400' => 'mes', 'Mapoly0019s0109' => 'mpo', 'Mapoly0028s0012' => 'mpo', 'Mapoly0109s0035' => 'mpo', 'Mapoly0119s0050' => 'mpo', 'MBI15_g43822_MAGBIO' => 'mbi', 'MBI19_g10809_MAGBIO' => 'mbi', 'MBI19_g10810_MAGBIO' => 'mbi', 'MBI19_g33011_MAGBIO' => 'mbi', 'MCO05G490' => 'mco', 'MCO15G552' => 'mco', 'MD02G1266900' => 'mdo', 'MD02G1267000' => 'mdo', 'MD07G1052100' => 'mdo', 'Medtr1157s0010' => 'mtr', 'Medtr1194s0010' => 'mtr', 'Medtr3g010820' => 'mtr', 'Medtr3g010840' => 'mtr', 'Medtr3g010850' => 'mtr', 'Medtr3g010900' => 'mtr', 'Medtr3g086440' => 'mtr', 'Medtr8g042770' => 'mtr', 'Medtr8g042780' => 'mtr', 'Medtr8g042820' => 'mtr', 'Medtr8g042870' => 'mtr', 'Medtr8g062990' => 'mtr', 'Medtr8g075280' => 'mtr', 'MELO3C011809.2' => 'cme', 'Migut.B01172' => 'egut', 'Migut.K00189' => 'egut', 'MSTRG.10761' => 'ama', 'MSTRG.16966' => 'ama', 'Nitab4.5_0000062g0620' => 'nta', 'Nitab4.5_0002687g0010' => 'nta', 'Nitab4.5_0002687g0020' => 'nta', 'Nitab4.5_0005848g0020' => 'nta', 'Nitab4.5_0008005g0020' => 'nta', 'Nn7g37210' => 'nnu', 'Nn7g37211' => 'nnu', 'Nn7g38498' => 'nnu', 'Oeu039191.1' => 'oeu', 'Oeu060848.1' => 'oeu', 'Os01g0268100' => 'osa', 'Os01g0279400' => 'osa', 'Os07g0180700' => 'osa', 'Os11g0134900' => 'osa', 'Os11g0135000' => 'osa', 'Os11g0135300' => 'osa', 'Os11g0135900' => 'osa', 'Os11g0136400' => 'osa', 'Os12g0132500' => 'osa', 'Os12g0132800' => 'osa', 'Os12g0133000' => 'osa', 'Os12g0133100' => 'osa', 'Os12g0133300' => 'osa', 'Peaxi162Scf00153g00416' => 'pax', 'Peaxi162Scf00220g00229' => 'pax', 'Peaxi162Scf00220g00237' => 'pax', 'PGR102G0534' => 'pgr', 'PGR102G1229' => 'pgr', 'PGR102G2386' => 'pgr', 'PGR142G0497' => 'pgr', 'PGSC0003DMG400007190' => 'stu', 'PGSC0003DMG400027509' => 'stu', 'PGSC0003DMG401003297' => 'stu', 'PGSC0003DMG402003297' => 'stu', 'Phvul.002G108300' => 'pvu', 'Phvul.005G012400' => 'pvu', 'Phvul.011G173100' => 'pvu', 'Phvul.011G173300' => 'pvu', 'Phvul.011G173400' => 'pvu', 'Phvul.011G189500' => 'pvu', 'Phvul.011G189600' => 'pvu', 'Phvul.011G189700' => 'pvu', 'Phvul.011G189800' => 'pvu', 'Phvul.011G189900' => 'pvu', 'Potri.006G026200' => 'ptr', 'Potri.008G010600' => 'ptr', 'Potri.010G248401' => 'ptr', 'Potri.016G024400' => 'ptr', 'Pp3c16_14400' => 'ppa', 'Pp3c25_6140' => 'ppa', 'Pp3c3_16020' => 'ppa', 'PRCOL_00000993' => 'pco', 'Prupe.2G056300' => 'ppe', 'Psat0s1896g0040' => 'psa', 'Psat0s909g0040' => 'psa', 'Psat4g143680' => 'psa', 'Psat4g143720' => 'psa', 'Psat5g092480' => 'psa', 'Psat5g220240' => 'psa', 'Psat5g225840' => 'psa', 'Psat5g225880' => 'psa', 'Psat5g225920' => 'psa', 'PSO017G2185' => 'pso', 'PSO017G6530' => 'pso', 'PSO170G1439' => 'pso', 'PSO210G0637' => 'pso', 'PSO210G0728' => 'pso', 'PSO210G4957' => 'pso', 'PSO339G1045' => 'pso', 'PSO339G1894' => 'pso', 'PSO384G1717' => 'pso', 'PSO384G4046' => 'pso', 'PSO675G4728' => 'pso', 'PSO675G4896' => 'pso', 'PSO675G5926' => 'pso', 'PSO675G7841' => 'pso', 'PSO832G0958' => 'pso', 'QL04p049367' => 'qlo', 'QL07p015430' => 'qlo', 'RcHm_v2.0_Chr1g0330291' => 'rch', 'Rhsim05G0161700' => 'rsi', 'Rhsim05G0161800' => 'rsi', 'Sabra06G0019300' => 'sbr', 'Sabra06G0019400' => 'sbr', 'Sabra08G0006400' => 'sbr', 'Sabra09G0013200' => 'sbr', 'Sabra16G0030300' => 'sbr', 'SalBow1G7329' => 'sbo', 'SalBow6G0270' => 'sbo', 'Sc13g0000710' => 'sci', 'Sc20g0000990' => 'sci', 'Sc21g0000260' => 'sci', 'Sed0006127' => 'sed', 'Sed0026867' => 'sed', 'SEGI_02040' => 'sgi', 'SEGI_06502' => 'sgi', 'SEGI_18363' => 'sgi', 'SEGI_18812' => 'sgi', 'SEGI_22930' => 'sgi', 'SEGI_28153' => 'sgi', 'SEGI_30094' => 'sgi', 'SEGI_40320' => 'sgi', 'SEGI_41229' => 'sgi', 'SGA_v2.0_scaffold123G33492' => 'sas', 'SGA_v2.0_scaffold141G35520' => 'sas', 'SGA_v2.0_scaffold5G02799' => 'sas', 'SHI21215' => 'shi', 'SMO014G0002' => 'smo', 'SMO111G0049' => 'smo', 'SMO118G0410' => 'smo', 'SMO137G0077' => 'smo', 'SMO137G0303' => 'smo', 'SMO137G0325' => 'smo', 'SMO304G0070' => 'smo', 'SMO343G0160' => 'smo', 'SMO367G1079' => 'smo', 'Solyc01g058360.1' => 'sly', 'Solyc01g096720.4' => 'sly', 'Solyc01g096730.2' => 'sly', 'Solyc01g096740.4' => 'sly', 'Solyc06g011660.3' => 'sly', 'Solyc06g048680.3' => 'sly', 'Solyc09g150122.1' => 'sly', 'Solyc10g076940.3' => 'sly', 'Solyc12g038220.3' => 'sly', 'Sopen01g040430' => 'spe', 'Sopen01g040440' => 'spe', 'Sopen01g040450' => 'spe', 'Sopen10g028650' => 'spe', 'Sp5g17450' => 'spa', 'Sp6g30270' => 'spa', 'Sp6g30280' => 'spa', 'TAR623G0745' => 'tar', 'TAR623G0807' => 'tar', 'TAR633G2121' => 'tar', 'THA.LOC104819100' => 'tha', 'THA.LOC104826689' => 'tha', 'THA.LOC104826690' => 'tha', 'THA.LOC104826692' => 'tha', 'THA.LOC104826693' => 'tha', 'Thecc.05G117000' => 'tca', 'Thecc.09G339100' => 'tca', 'Thecc.09G339200' => 'tca', 'Thecc.10G109500' => 'tca', 'Thhalv10013388m.g' => 'esa', 'Thhalv10013417m.g' => 'esa', 'Thhalv10015125m.g' => 'esa', 'TPR.G11413' => 'tpr', 'TPR.G11414' => 'tpr', 'TPR.G25003' => 'tpr', 'TPR.G31178' => 'tpr', 'TPR.G36441' => 'tpr', 'TPR.G5066' => 'tpr', 'TPR.G5103' => 'tpr', 'TPR.G5127' => 'tpr', 'TPR.G6856' => 'tpr', 'TPR.G6864' => 'tpr', 'TPR.G6892' => 'tpr', 'TPR.G6900' => 'tpr', 'TPR.G6906' => 'tpr', 'TPR.G7281' => 'tpr', 'TWI38G0510' => 'twi', 'TWI38G0532' => 'twi', 'TWI38G2097' => 'twi', 'TWI63G0279' => 'twi', 'TWI79G1578' => 'twi', 'unitig_26.g9284' => 'ugi', 'unitig_746.g26556' => 'ugi', 'unitig_899.g15478' => 'ugi', 'vmacro19562' => 'vma', 'vmacro19563' => 'vma', 'vmacro19564' => 'vma', 'VMungo1080G0606' => 'vmu', 'VMungo1127G0390' => 'vmu', 'VMungo1127G0577' => 'vmu', 'VMungo1127G0779' => 'vmu', 'VMungo1127G0937' => 'vmu', 'Zm00001eb038000' => 'zma', 'Zm00001eb093430' => 'zma', 'Zm00001eb093440' => 'zma', 'Zm00001eb128730' => 'zma', 'Zm00001eb129050' => 'zma', 'Zm00001eb129340' => 'zma', 'Zm00001eb129500' => 'zma', 'Zm00001eb132340' => 'zma', 'Zm00001eb133440' => 'zma', 'Zm00001eb163460' => 'zma', 'Zm00001eb196170' => 'zma', 'Zm00001eb196180' => 'zma', 'Zm00001eb332620' => 'zma', 'Zm00001eb406090' => 'zma' ) $gf_id = 'HOM05D001269' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001269' ) $data_identifier = 'HOM05D001269' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 2, 'aag' => (int) 4, 'ach' => (int) 3, 'amhyb' => (int) 2, 'aly' => (int) 4, 'aox' => (int) 3, 'arhy' => (int) 6, 'ath' => (int) 3, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 5, 'bca' => (int) 13, 'bol' => (int) 14, 'bra' => (int) 8, 'can' => (int) 8, 'cansat' => (int) 6, 'chi' => (int) 3, 'cru' => (int) 5, 'car' => (int) 7, 'ccan' => (int) 4, 'cde' => (int) 1, 'cfa' => (int) 6, 'ccl' => (int) 2, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 1, 'camsi' => (int) 2, 'dca' => (int) 9, 'din' => (int) 2, 'dzi' => (int) 4, 'eca' => (int) 4, 'bvu' => (int) 2, 'egr' => (int) 8, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 9, 'ghi' => (int) 6, 'gra' => (int) 6, 'vvi' => (int) 6, 'han' => (int) 13, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 2, 'sun' => (int) 7, 'lal' => (int) 14, 'lja' => (int) 11, 'lonja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 2, 'mpo' => (int) 4, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 3, 'mtr' => (int) 13, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 5, 'nnu' => (int) 3, 'oeu' => (int) 2, 'osa' => (int) 13, 'pax' => (int) 3, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 10, 'ptr' => (int) 4, 'ppa' => (int) 3, 'pco' => (int) 1, 'ppe' => (int) 1, 'psa' => (int) 9, 'pso' => (int) 15, 'qlo' => (int) 2, 'rch' => (int) 1, 'rsi' => (int) 2, 'sbr' => (int) 5, 'sbo' => (int) 2, 'sci' => (int) 3, 'sed' => (int) 2, 'sgi' => (int) 9, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 9, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 3, 'tha' => (int) 5, 'tca' => (int) 4, 'esa' => (int) 3, 'tpr' => (int) 14, 'twi' => (int) 5, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 5, 'zma' => (int) 14 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb406090' $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